===============================
BiocCheckGitClone('epiSeeker')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epiSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiSeeker’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epiSeeker’ can be installed ... OK
* checking installed package size ... INFO
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 4.9Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘RSQLite’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [14s/14s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' calls not declared from:
‘GEOmetadb’ ‘GEOquery’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [50s/50s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'arrange.GRanges.Rd'
‘.data’ ‘...’ ‘.by_group’
Undocumented arguments in Rd file 'filter.GRanges.Rd'
‘.data’ ‘...’ ‘.by’ ‘.preserve’
Undocumented arguments in Rd file 'mutate.GRanges.Rd'
‘.data’ ‘...’ ‘.by’ ‘.keep’ ‘.before’ ‘.after’
Undocumented arguments in Rd file 'rename.GRanges.Rd'
‘x’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [14s/14s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] ERROR
Running examples in ‘epiSeeker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrange.GRanges
> ### Title: arrange granges object
> ### Aliases: arrange.GRanges
>
> ### ** Examples
>
> require(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> peakfile <- system.file("extdata", "sample_peaks.txt", package="epiSeeker")
> peak <- readPeakFile(peakfile)
> arrange(peak, seqnames)
Error in arrange(peak, seqnames) : could not find function "arrange"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotateSeq 16.416 0.504 16.921
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [109s/109s]
[109s/109s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker.Rcheck/00check.log’
for details.
===============================
BiocCheck('epiSeeker_0.99.3.tar.gz')
===============================
── Installing epiSeeker ────────────────────────────────────────────────────────
✔ Package installed successfully
── epiSeeker session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiZdQML/file28a2cd3ec8f4c9/epiSeeker
→ BiocVersion: 3.22
→ Package: epiSeeker
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3952/2175e71e2faff98adfc96c5e6fdf6990ffdd94c1/epiSeeker.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpiZdQML/file28a2cd3ec8f4c9/epiSeeker
→ installDir: /tmp/RtmpiZdQML/file28a2cd5f98adbb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on epiSeeker ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: GeneRegulation
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (34%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• epiSeeker.rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of epiSeeker...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/enrichOverlap.R (line 221, column 18)
• ...
• R/utilities.R (line 495, column 27)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• annotateSeq.R (line 175, column 38)
• ...
• utilities.R (line 1184, column 36)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/annotateSeq.R (line 116, column 9)
• ...
• cat() in R/utilities.R (line 648, column 21)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/dplyr-verb.R (line 13, column 8)
• ...
• R/utilities.R (line 543, column 18)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/bmData.Rd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressWarnings() in R/addGeneAnno.R (line 31, column 9)
• ...
• suppressMessages() in R/utilities.R (line 436, column 25)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 45
functions greater than 50 lines.
The longest 5 functions are:
• plotBmProf.internal() (R/plotBmProf.R): 394 lines
• ...
• getGenomicAnnotation() (R/getGenomicAnnotation.R): 185 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getPromoters.Rd
• ...
• plotAnnoPie-methods.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 561 lines (6%) are > 80 characters long.
First few lines:
• R/addGeneAnno.R#L24 message("geneID type is not supp ...
• ...
• vignettes/epiSeeker.rmd#L781 Here is the output of `sessionInfo()` on ...
i NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
First few lines:
• R/epiSeeker-package.R#L41 #' \item{areaStat}{ The sum of the tes ...
• ...
• R/getGenomicAnnotation.R#L195 annotation[j] <- lbs ...
i NOTE: Consider multiples of 4 spaces for line indents; 1941 lines (21%) are
not.
First few lines:
• R/AllGenerics.R#L15 function(x, r = 0.2, cex = 1.2, ...) ...
• ...
• vignettes/epiSeeker.rmd#L689 verbose = FALSE) ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 16 NOTES
i See the epiSeeker.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.